RetrogeneDB ID: retro_cjac_460

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:123608215..123609480(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KHSRP
• Ensembl ID: ENSCJAG00000016627
• Aliases: None
• Description: None

Sequence

>retro_cjac_460
GGAGGCGAACAAATTAACAAAATCCAACGGGATTCAGGCTGTAAAATACAGATTTCTCCAGACACTGGTGGCCTACCCGA
GCGCAGTGTGTCCTTGACAGGAGCTCCAGAATCTCTCCAGAGAGTGAAGATGATGCTGGATGACATTATGTCTCGGGGTC
GTGGGGGCCCCCGAGGACAGTTCCACGACAATGCCAGCGGGGGCCAGAACCGCACCAGTGCAGGAGATTATGATACCCGC
AGGCGACGCCGGCCTGGTCATCGGCAAGGACCGTGAGACCGTTAAGCAGCTGCAAGGAACGCGCTGGAGTGAAGATGATC
TTAATTCATGATGGTTCTCAGAATTCGAATGTGGACAAGCCTCTCCGGATCAATGGGGATCCTTAGAAAGTGCAGCAAGC
CTGCAGATGGTGATAGACATCCTCTGAGAACGTGACCAAGGCGGCTTTGGGGACCAGAATGAGTAAGAACCTCAGATTGG
CATCGATGTGCGGGTGCCCAGGATTCTGTCGGTGTGGTCATTGGCCAGAGAGGAGAGATGATCCAGAAGATCCAGAATGA
TGCTGGTGGGCCGATACGGTTCCAGCAAAATGACCGGACAGGGCCCAAGATTGTTCATAGAATGGGGCCCCCAGACAGGT
GCGAGTACACGGCCCGGATGGTCAGTGACCTCCTCCACAACCTCAGAAGTGGTCCCCCAGGCTCTCCACGGGGTCCACAC
ATGCCCCGGGGAGTCCGAGGCGAAGGAAGAGGCCAAAGCAACTGGGGCCCTCTGGCGGGAGATGATCTTCTCCACTCCCA
CTCACAAGTGAGGCCTGGTCATGGGCCGAGGTGGCGAGAACGTGAAAGCCATAAGCCAGCAGATGGGAGCCTTCCTAGAG
ATCATCCAGCAGATGCCACCCAATGGGGACCCCAACTTCAAGTTGTTCATCATCCGGGGTTCGCCCCAGCAGATTGAGGA
GCAGCTTATCGAGGAGATCGAAGGTTCTCTCTGCCCTGTTGGACCAGGCCCAGGCGCCCCATGCCCTGCTGGCCCAAATG
CGGTCCTTCAACCCTGGGCCCTTCAACCAGGGCCACCTGGGGCTCCATCGCATGCCAGGGGGTTCCCTCCTCACCAGTAC
CCACCCCAGGGGTTGGGGCAATACCTACCCCCAGGGCCACCCTCTGGCTCCTCACGACCCAAGCAAAGAAGTTGCGGATG
CCGCGGACCCCAACGCTGCGTGGGACCGCCTCTATTTCTACTAAAAACCGAAATTCCCTGGACCA

Alignment

ORF - retro_cjac_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 67.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  GGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQN
          GGEQINKIQ.DSGCK.QISPD.GGLPERSVSLTGAPES.Q..KMMLDDI.SRGRGGP.GQFHDNA.GGQN
Retrocopy GGEQINKIQRDSGCKIQISPDTGGLPERSVSLTGAPESLQRVKMMLDDIMSRGRGGPRGQFHDNASGGQN

Parental  GT-VQEIMIPAGKAGLVIGKGGETIKQLQ-ERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQAC-EMV
          .T.VQEIMIPAG.AGLVIGK..ET.KQLQ.ERAGVKMILI.DGSQN.NVDKPLRI.GDP.KVQQAC..MV
Retrocopy RT>VQEIMIPAGDAGLVIGKDRETVKQLQ>ERAGVKMILIHDGSQNSNVDKPLRINGDP*KVQQAC<QMV

Parental  MDILRERDQGGFGDRNEYGSRIGGGIDVPVPR-HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEK
          .DIL.ERDQGGFGD.NE....I..GIDV.VPR..SVGVVIG..GEMI.KIQNDAG..I.F.Q.D.TGP.K
Retrocopy IDIL*ERDQGGFGDQNE*EPQI--GIDVRVPR<DSVGVVIGQRGEMIQKIQNDAGGPIRFQQNDRTGP-K

Parental  IAHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNW-GPPGG-EMTFSIPTHKC
          I.H.MGPPDRCE..AR...DLL..LRSGPPG.P.GP.MP.G.RG.GRGQ.NW.GP.GG.EM.FS.PTHK.
Retrocopy IVHRMGPPDRCEYTARMVSDLLHNLRSGPPGSPRGPHMPRGVRGEGRGQSNW<GPSGG<EMIFSTPTHK*

Parental  GLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGP
          GLV.GRGGENVKAI.QQ.GAF.EI..Q.PPNGDPNFKLFIIRGSPQQI....QLIEE.IEG.LCPVGPGP
Retrocopy GLVMGRGGENVKAISQQMGAFLEIIQQMPPNGDPNFKLFIIRGSPQQIE--EQLIEE-IEGSLCPVGPGP

Parental  GGPGPAGP-MGPFNPGPFNQ-GPPGAPPHAGGPPPHQYPPQ-GWGNTYPQWQPPAPHDPSKAAAAAADPN
          G.P.PAGP.M..FNPGPFNQ.GPPGAP.HA.G.PPHQYPPQ.GWGNTYPQ..P.APHDPSK..A.AADPN
Retrocopy GAPCPAGP>MRSFNPGPFNQ<GPPGAPSHARGFPPHQYPPQ>GWGNTYPQGHPLAPHDPSKEVADAADPN

Parental  AAWAAYYSHYYQQPPGP
          AAW...Y.......PGP
Retrocopy AAWDRLYFY*KPKFPGP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	13.58 RPM
SRP051959_heart	0.00 RPM	12.91 RPM
SRP051959_kidney	0.00 RPM	15.46 RPM
SRP051959_liver	0.00 RPM	9.68 RPM
SRP051959_lung	0.00 RPM	11.58 RPM
SRP051959_lymph_node	0.00 RPM	14.29 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.09 RPM
SRP051959_spleen	0.00 RPM	13.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_460 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016627	1 retrocopy	retro_cjac_460 ,
Callithrix jacchus	ENSCJAG00000020542	1 retrocopy	retro_cjac_3887,
Homo sapiens	ENSG00000088247	1 retrocopy	retro_hsap_4142,
Macaca mulatta	ENSMMUG00000005597	1 retrocopy	retro_mmul_1185,
Monodelphis domestica	ENSMODG00000001952	1 retrocopy	retro_mdom_1386,
Otolemur garnettii	ENSOGAG00000008073	1 retrocopy	retro_ogar_884,
Pan troglodytes	ENSPTRG00000010364	1 retrocopy	retro_ptro_2814,